diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix')
-rw-r--r-- | nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix | 33 |
1 files changed, 33 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix new file mode 100644 index 000000000000..880ea77e9d24 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix @@ -0,0 +1,33 @@ +{lib, stdenv, fetchurl, jre, makeWrapper}: + +stdenv.mkDerivation rec { + pname = "picard-tools"; + version = "3.1.1"; + + src = fetchurl { + url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; + sha256 = "sha256-FcefUf0KwAEEn53XubrB2991ncsCMKicf20fJG6LurQ="; + }; + + nativeBuildInputs = [ makeWrapper ]; + buildInputs = [ jre ]; + + dontUnpack = true; + + installPhase = '' + mkdir -p $out/libexec/picard + cp $src $out/libexec/picard/picard.jar + mkdir -p $out/bin + makeWrapper ${jre}/bin/java $out/bin/picard --add-flags "-jar $out/libexec/picard/picard.jar" + ''; + + meta = with lib; { + description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF"; + license = licenses.mit; + homepage = "https://broadinstitute.github.io/picard/"; + sourceProvenance = with sourceTypes; [ binaryBytecode ]; + maintainers = with maintainers; [ jbedo ]; + mainProgram = "picard"; + platforms = platforms.all; + }; +} |